Analysis of the algorithm: From rankings to backup genes.

Ranking section

Table 1. Performance summary for every kernel and net before integration.

Net	Kernel	tpr_down_ci_0.95	tpr_up_ci_0.95	fpr_down_ci_0.95	fpr_up_ci_0.95	f
biological_process	ct	0.129933211900425	0.168184578020644	0.000610526140154569	0.00108986398338977	0.150717703349282
biological_process	el	0.0103155339805825	0.0242718446601942	0.000470839005909212	0.00207790951652707	0.0179900744416873
biological_process	ka	0.13357619914997	0.171220400728597	0.000453997019585433	0.000792565544613928	0.173853989813243
biological_process	rf	0.00364077669902913	0.0121359223300971	0.0032327164803559	0.00915573299934875	0.00236406619385343
cellular_component	ct	0.0679459951456311	0.0964805825242718	0.000410515254668196	0.000876423173383597	0.099361249112846
cellular_component	el	0.000606428138265616	0.00667070952092177	0.00112426457832003	0.00664783948961097	0.00287769784172662
cellular_component	ka	0.0703731796116505	0.098316140776699	0.000449080427074444	0.00113529563766816	0.0987569060773481
cellular_component	rf	0.00303214069132808	0.0109157064887811	0.00328628579555785	0.0112871370691079	0.00222613857712643
disease	ct	0.275342465753425	0.342482876712329	0.000640083721977323	0.000916941227293608	0.309914642153644
disease	el	0.0574948665297741	0.0910506502395619	0.00126664553334461	0.00255318721730125	0.0562560620756547
disease	ka	0.291078767123288	0.358236301369863	0.000418594675501282	0.000645559723401084	0.3674228337672
disease	rf	0.00684462696783025	0.0184804928131417	0.00836853694538719	0.0199558238527466	0.00234350909651557
gene_PS	el	0.328793774319066	0.417315175097276	0.00129831492092424	0.0017672005543494	0.28044537230341
gene_PS	ka	0.374489299610895	0.441658560311284	0.000945232576312484	0.00136233625132515	0.331782945736434
gene_PS	rf	0.316147859922179	0.401750972762646	0.00108739758940861	0.00158739947238892	0.294162244124337
gene_TF	el	0.00714285714285714	0.0642857142857143	0.0108323768923867	0.07456113023993	0.00562429696287964
gene_TF	ka	0.0428571428571429	0.135714285714286	0.0445972017270591	1	0.00450704225352113
gene_TF	rf	0	0.0428571428571429	0.00294009946985845	0.0610203858556047	0.00710059171597633
gene_hgncGroup	el	0.0810611643330877	0.116433308769344	0.00060002450289424	0.00146197308897185	0.105263157894737
gene_hgncGroup	ka	0.111274871039057	0.148857774502579	0.00041101629047259	0.000921509720798742	0.155866900175131
gene_hgncGroup	rf	0.0913780397936625	0.1319270449521	0.000501255443989809	0.00101504227407936	0.12683313515656
genetic_interaction_effect_bicor	ct	0.0311332503113325	0.0510585305105853	0.000476413172818198	0.00130950977134097	0.0473330978452844
genetic_interaction_effect_bicor	el	0.0012453300124533	0.0087173100871731	0.000534891137720699	0.00228728707267133	0.00635144671841919
genetic_interaction_effect_bicor	ka	0.0336239103362391	0.0516967621419676	0.000425586655660731	0.00102916662199972	0.0520361990950226
genetic_interaction_effect_bicor	rf	0.00062266500622665	0.0049813200498132	0.00114971377421397	0.00631257839048916	0.0018984337921215
molecular_function	ct	0.0667483159828536	0.093692590324556	0.000468532512745182	0.00121478915970971	0.0877887788778878
molecular_function	el	0.000611995104039168	0.00611995104039168	0.00129952907966073	0.00750156313894129	0.00234100663285213
molecular_function	ka	0.0642988364972443	0.0918707899571341	0.000616272149073514	0.00133602799877165	0.0818494220556076
molecular_function	rf	0.570991432068543	0.61750305997552	0.552912978670079	0.598954939387144	0.00178251156062467
pathway	el	0.179447852760736	0.248504601226994	0.000504021062954794	0.00108155231653206	0.239600665557404
pathway	ka	0.193251533742331	0.271472392638037	0.000674747519618379	0.00166092025703366	0.250587314017228
pathway	rf	0.174846625766871	0.243865030674847	0.000577488539927865	0.00138405038160374	0.233360723089564
phenotype	ct	0.262998647734956	0.32657200811359	0.000624453974471132	0.000923017314027199	0.296368989205103
phenotype	el	0.154158215010142	0.203515889114266	0.000588711418408546	0.00104019164195117	0.184677149548344
phenotype	ka	0.225152129817444	0.290736984448952	0.000406192442441698	0.000595342524899359	0.308575803981623
phenotype	rf	0.0189189189189189	0.0351351351351351	0.0166236586125933	0.0301827480511077	0.00222890894906943
protein_interaction	el	0.263379434756464	0.317498496692724	0.00159482896820349	0.00218543501846686	0.180760138206947
protein_interaction	ka	0.260974143114853	0.309696331930247	0.000635557941268034	0.000962412617247253	0.272212790039615
protein_interaction	rf	0.271033653846154	0.330528846153846	0.000719786547574045	0.000999840722581659	0.281377066955815

Table 2. Performance summary for every kernel after integration

Integration	Kernel	tpr_down_ci_0.95	tpr_up_ci_0.95	fpr_down_ci_0.95	fpr_up_ci_0.95	f
integration_mean_by_presence	ct	0.330137807070102	0.384661473936489	0.000623857268862939	0.000883082050345744	0.335810624827966
integration_mean_by_presence	el	0.00119331742243437	0.00715990453460621	0.000259008223427741	0.00709247560465173	0.00314253647586981
integration_mean_by_presence	ka	0.340880597014925	0.404194029850746	0.000332871176110626	0.000521670865064966	0.41851368970013
integration_mean_by_presence	rf	0.0835820895522388	0.112238805970149	0.000507270128075513	0.000936150491933279	0.10651267244145
mean	ct	0.386458957459557	0.449985020970641	0.000474681835364427	0.000703060912230534	0.423473901503981
mean	el	0.0967164179104478	0.154029850746269	0.000493946561083489	0.000760712840328014	0.160628844839371
mean	ka	0.367746268656716	0.436417910447761	0.000480110055997452	0.000713535359131042	0.415700267618198
mean	rf	0.196417910447761	0.266283582089552	0.000494972437271518	0.000750466901900077	0.267954911433172

Backup Pairs Coverage By Layer Non integrated

Backup Pairs Coverage By Layer Integrated

Distribution of ranks in dataset by non integrated kernels

Distribution of ranks in dataset by Integrated kernels

ROC-AUCs for Non-integrated kernel and layer

ROC-AUCS for integrated kernels

CDF plots of non integrated kernels

ROC plots of non integrated kernels

ROC plots of integrated kernels

CDF plots of integrated kernels